Red Alert 3 retains the core RTS mechanics of the Command & Conquer series. Warring factions harvest resources using vulnerable collectors and then use those resources to construct military bases and forces on-site. Structures form a shallow but wide tech tree with a variety of units and elusive superweapons. Weapon types are specialized to the point where a rifleman can withstand direct hits from an anti-tank cannon. Red Alert 3 '​s major refinements are the addition of the Empire of the Rising Sun to the factions of the sub-series (similar to what Tiberium Wars did with the Scrin faction), a co-operative campaign, and expanded naval warfare.

The "single-player" campaign is now fully co-operative. Each mission is played alongside an ally. When played online, this is another human player. Offline it is one of several computer-controlled characters. Teams share income and generally start with the same forces. Computerized characters can be given simple commands, such as an order to take a specific position or to strike a specific target. The campaign has nine missions for each side. Each side's plotlines are mutually exclusive, unlike Tiberium Wars and its preceding and following expansion packs, but like most of the other Command & Conquer games.

Naval warfare is emphasized as another front. Executive producer Chris Corry has stated that many units are now amphibious, trading effectiveness for increased flexibility. Buildings and entire bases can be constructed on water, save for such things as ground or naval unit production facilities (e.g. tank factories are ground-only, but Tsunami tanks are amphibious and can be produced in Naval Yards),[13] and players who "ignore the ocean [are] likely forfeiting a significant part of their potential economy to their opponents." Further stressing this is the fact that, despite some campaign maps being entirely land based, all multiplayer maps have significant bodies of water in them.